Doing more reading on the aroma forum I see question #2 stated above
dovetails with the idea of "filtering" probes.
I noticed this statement in two places in the Vignettes:
"The full CDF contains what the default one does plus more. We are always
using the full CDF. If we want to do filtering, we do it afterward."
But I can not find any examples, or code, that performs this filtering.
Why is the Full CDF recommended given the fact that Affy indicates several
probes are of poor quality? Is there a way to assess poor quality probes
and filter them from the SNP 6.0 array? Would this filtering take place
after CRMAv2 has run?
Thanks in advance for any clarity on these issues,
Greg
On Feb 23, 2011 4:02pm, Gregory W <greg.d.w...@gmail.com> wrote:
Hello,
I was hoping to get some information about how to manipulate
AromaUnitTotalCnBinarySets.
I've already performed CRMAv2 on all the affy platforms in my study.
I load the results into an R session with:
> tags
> dsT
> print(dsT)
> dsC
> dsC$total
I have normal and tumor replicates for a particular patient. I grab
these data by:
> normals.indx
> normals
And similarly for the tumors. This is what normals and tumors
contains:
> normals
. AromaUnitTotalCnBinarySet:
. Name: MyStudy
. Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
. Full name: MyStudy,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
. Number of files: 2
. Names: Normal_Rep1, Normal_Rep2
. Path (to the first file): totalAndFracBData/MyStudy,ACC,ra,-
XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6
. Total file size: 14.35 MB
. RAM: 0.00MB
> tumors
. AromaUnitTotalCnBinarySet:
. Name: MyStudy
. Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
. Full name: MyStudy,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
. Number of files: 2
. Names: Tumors_Rep1, Tumors_Rep2
. Path (to the first file): totalAndFracBData/MyStudy,ACC,ra,-
XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6
. Total file size: 14.38 MB
. RAM: 0.00MB
I see there's a function getAverageFile that allows me to do this:
> normals.average
> normals
and similarly for tumors. Then I can take these results and pass them
to CbsModel:
> cbs
HOWEVER, even though my replicates are from the same sample, they were
processed using different protocols. So instead of averaging the
normals and then averaging the tumors, i would like to take the
respective ratios and then average the ratios.
I can accomplish this in a round about way by using writeDataFrame and
loading it back into R and then manipulating the data. But then the
data isn't in the right format for CbsModel since its been ratio-ized
and is no longer two AromaUnitTotalCnBinarySets.
1- Is there a way to perform an average of the ratios and then pass
this into the CbsModel??
Additionally, there are several Units (or probes) that I want to
disqualify, for instance maybe by setting them to 1 for each tumor and
normal replicate.
2- Is there a way to set
> CN_473963
> CN_473964
> CN_473965
to 1 for each file Normal_Rep1, Normal_Rep2, Tumor_Rep1 and Tumor_Rep2
file in the AromaUnitTotalCnBinarySet??
Thank you!
Greg
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